X-Files 3 (Fan Made)
by Shatha
Summary: Just when Mulder and Scully thought they left the life they had with the FBI and The X-Files behind them a new case comes crashing at them. This time involving their son, William. The aliens have improved their technology greatly since their last visit to Earth and their new mission: create an army. An army of superhumans.
1. Chapter 1

Chapter 1: The Beginning Of A New Era

"Mulder! Mulder wake up!"

"Wh-What's going on?"

"Get up and get dressed as QUICK as you can we have to go somewhere"

"Go where? Its to 2 in the morning for Christ's sake what's going on?"

"I'll tell you everything in the car let's just go"

It has been 8 years since Mulder and Scully left the force and decided to finally settle down. Mulder and Scully had their first child, William, years ago but decided that putting the boy up for adoption was best for the child. William was adopted by a nice couple that were unable to have children and lived with them in Minnesota. The last time they saw their child was 2 years ago. The couple decided it was best if Mulder and Scully didn't visit William since he was only a child and would have many questions to ask if he knew he was adopted. He wasn't the only one. Scully had been abducted by aliens 9 years ago and had brutal tests performed on her which she believes led to her pregnancy. Till this day she had tens of questions she didn't know the answers to about William, questions she sometimes didn't _want_ to know the answers to out of fear of knowing who or what William was.

Scully had been waiting in the car for about 10 minutes until Mulder finally arrived. Mulder's tie was loose around his neck and his hair was still messy from being asleep for a long time.

"Alright i'm here tell me what is going on" said Mulder closing the passenger seat door.

"To be honest _I _don't even entirely know what's happening. I got a call from Skinner saying that-"

"Wait _Skinner _called? Last time I ever talked to the man was back when I was chasing UFOs"

"That is why I knew it was important. It is about William. He's gone missing. He says it doesn't look like any ordinary missing person's case. He thinks Will was abducted, he thinks this is an X-File."


	2. Chapter 2

Chapter 2

Mr and Mrs Smith, the couple that adopted William, lived in a ranch that was a 45 minute drive from where Scully and Mulder lived. Skinner had called them an hour before telling them that William had gone missing and that he was appointed to the case since he had previous experiences working cases that seemed too weird for others to handle.

Scully had been so nervous and scared throughout the drive she almost crashed into not one but two cars in just a 20 minute period. Mulder decided it was best if he took the wheel.

"Its alright Dana. We'll get him back"

The ranch was a mess. The second floor was almost completely burnt to ashes and what remained of the house seemed like it could collapse any minute. Scully stared in horror at the sight of the house and a million thought went rushing through her head all at once. If this really was the work of extraterrestrials, why did they wait so long to abduct William, why now? Scully suddenly recalled her encounter with the aliens and was even more horrified. Could they be performing the same brutal tests on William right this second?

"Scully! Mulder!"

Scully turned around and saw Skinner rushing over to them. "Im really sorry about what happened to your son. I will try to do _everything _I can to get him back" he said laying his hand on Scully's shoulder. "Im really sorry to sound inconsiderate but we can't waste anymore time we have to get started investigating this case immediately. I know this must be really hard for you but I need yo- _William_, needs you two to stop being his parents for the time being and start being detectives Mulder and Scully. I couldn't think of anyone who could be more suitable for solving this case other than you two."

"We understand. What happened here? The whole second floor is in ashes was there a fire?" asked Mulder.

"Nope. No fire. According to a couple that were driving on the highway, they saw a "beam of green light come down from the sky" in the direction of the ranch. As soon as I heard them say that I knew exactly what we were dealing with. Ive sent the Smiths down to the police station. They're going to give them a place to stay until we get this mess repaired. I got the forensic team down here to sweep for evidence or something that would help us, but they found nothing. Just a pile of ash. Mrs Smith said that William was sleeping in his room when he was taken. I know this must be overwhelming for the both of you, but do you have any idea where we can start?"

"I'll need to review all our previous X-File cases and see if anything was remotely similar to this" said Mulder.

"Of course ill call the FBI to get all the files ready for you. Should I send them back to your place?"

"No, we'll be needing my basement office back, its the only place I can work properly."

Skinner smiled, "Sure thing Mulder. Welcome back to the bureau."

Scully hadn't said a word through all the entire drive back home. Every time she tried to forget about it and focus on the case an image of the aliens inserting chips into William's head kept appearing in her mind. Mulder knew he should have probably taken the case himself and left Scully out of this since it was very emotional to her but he knew how hard headed Dana was and that she wouldn't agree to stepping down, but he also knew that it was always Mulder and Scully, the unstoppable duo, he provided his crazy alien conspiracy theories and she would say that that idea was mad and would give her scientific opinion and both their theories would meet halfway and the case would be solved. He couldn't do it alone.

Scully had calmed down since then and her and Mulder spent the next 2 days reading old case files in their basement office. The place hadn't changed a bit. And neither did the people working there. Mulder overheard a couple of young agents call him "Spooky Mulder". It didn't bother him one bit, on the contrary he actually missed it. He missed being called spooky, missed running after UFOs and Cigarette Smoking Man.

"Mulder. Wake up. Alvin Kersh is going to be here in an hour". Scully placed a cup of coffee on Mulder's desk. Mulder had been working late in his office reviewing previous case files all night and accidentally fell asleep. "Im up I'm up. Wait, Alvin Kersh? The Deputy Director of the FBI? What does he want?" "Skinner told me he just wanted to check how everything is going. He was the one that closed the X-Files for good. He wanted to see what case reopened them again. He isn't too pleased about us being reassigned to the X-Files.." Just as Mulder opened his mouth to reply with a sarcastic comment about Kersh, Scully said "Save your smart remarks Mulder, the guy _did _help you get out of prison once. Anyway lets get back to the case. Find anything interesting in our old files?"

"Nothing. I've been up all night looking at them. We had a few abduction cases but nothing like this. The beam of green light the two witnesses said they saw was never seen before. I don't know what to next Scully. Its not like we can start a search mission or something and we have a little to go on. What do you think?"

"I don't really know Mulder. What really intrigues me is why they chose to take him now. I mean why not after he was born or maybe a year after. Why now all of a sudden? He's just a child!"

"I don't know yet. But we'll find out and we'll get him back. That much I _do _know"


End file.
